AutoDock Vina

Differentiable, Hardware Accelerated, Molecular Dynamics

End-To-End Molecular Dynamics (MD) Engine using PyTorch

Some useful RDKit functions

Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

Reaction fingerprints, atlases and classification. Code complementing our Nature Machine Intelligence publication on "Mapping the space of chemical reactions using attention-based neural networks" (http://rdcu.be/cenmd).

Molecular Processing Made Easy.

A Pharmacophore MultiToolkit designed to simplify and streamline the detection, generation, analysis, comparison, and application of pharmacophore models in drug-design strategies.

Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping

Source code for molecular graphics program UCSF ChimeraX

Molsystem provides a general class for handling molecular and periodic systems

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

IF-SitePred is a method for predicting ligand-binding sites on protein structures. It first generates an embedding for each residue of the protein using the ESM-IF1 (inverse folding) model, then performs point cloud clustering to identify binding site centers.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

A comprehensive macromolecular library

An automated framework for generating optimized partial charges for molecules